fix: restore PDFParser

news/fix-pdfparser-import.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Restores a module the package __init__ already referenced; no user-facing change since diffpy.cmipdf has not been released.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/cmipdf/pdfparser.py

@@ -0,0 +1,171 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 Simon Billinge.
+# All rights reserved.
+#
+# File coded by: Caden Myers, Simon Billinge, and members of the Billinge
+#                group.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.cmipdf/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""This module contains parsers for PDF data.
+
+PDFParser is suitable for parsing data generated from PDFGetN and
+PDFGetX.
+
+See the class documentation for more information.
+"""
+
+__all__ = ["PDFParser"]
+
+import re
+from pathlib import Path
+
+from diffpy.srfit.fitbase.profileparser import ProfileParser
+
+_FLOAT_RX = r"[-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][-+]?\d+)?"
+
+
+class PDFParser(ProfileParser):
+    """Parser for PDF diffraction pattern data.
+
+    PDFgetX and PDFgetN write their header as plain ``name = value``
+    pairs, including ``stype = X`` or ``stype = N`` for the scattering
+    type, so this class parses files identically to ``ProfileParser``
+    for those. Some facilities instead prepend a
+    free-text instrument comment, so this class also falls back to
+    scanning that comment for the scattering type, ``qmin``, ``qmax``,
+    ``qdamp``, and ``qbroad`` when they are not already present as
+    ``name = value`` pairs.
+
+    Attributes
+    ----------
+    _format
+        The name of the data format that this parses (string, default
+        ``""``). The format string is a unique identifier for the data
+        format handled by the parser.
+    _banks
+        The data from each bank. Each bank contains a
+        (x, y, dx, dy) tuple:
+        x
+            A numpy array containing the independent
+            variable read from the file.
+        y
+            A numpy array containing the profile
+            from the file.
+        dx
+            A numpy array containing the uncertainty in x
+            read from the file. This is None if the
+            uncertainty cannot be read.
+        dy
+            A numpy array containing the uncertainty read
+            from the file. This is None if the uncertainty
+            cannot be read.
+    _x
+        The independent variable from the chosen bank.
+    _y
+        The profile from the chosen bank.
+    _dx
+        The uncertainty in independent variable from the chosen bank.
+    _dy
+        The uncertainty in profile from the chosen bank.
+    _meta
+        A dictionary containing metadata read from the file.
+
+    General Metadata
+    -----------------
+    filename
+        The name of the file from which data was parsed. This key
+        will not exist if data was not read from file.
+    nbanks
+        The number of banks parsed.
+    bank
+        The chosen bank number.
+
+    Metadata
+    --------
+    stype
+        The scattering type ("X", "N").
+    qmin
+        The minimum scattering vector (float).
+    qmax
+        The maximum scattering vector (float).
+    qdamp
+        The Q-resolution damping factor (float).
+    qbroad
+        The Q-resolution broadening factor (float).
+
+    These, along with any other ``name = value`` pairs in the header,
+    may appear in the metadata dictionary.
+    """
+
+    _format = "PDF"
+
+    def _parse_metadata(self, filename):
+        """Return the metadata read from a PDFgetX or PDFgetN header.
+
+        This calls ``ProfileParser``'s ``name = value`` based parsing
+        first, then falls back to scanning the free-text instrument
+        comments some facilities prepend to their files for the
+        scattering type and Q-resolution parameters that
+        such comments are not already covered by a ``name = value``
+        pair.
+
+        Parameters
+        ----------
+        filename : str or Path
+            The name of the file to parse.
+
+        Returns
+        -------
+        dict
+            The metadata read from the file header.
+        """
+        metadata = super()._parse_metadata(filename)
+        self._parse_comment_metadata(Path(filename).read_text(), metadata)
+        return metadata
+
+    @staticmethod
+    def _parse_comment_metadata(header_text, metadata):
+        """Fill in stype, qmin, qmax, qdamp, and qbroad from free-text
+        instrument comments, without overwriting values already found by
+        the ``name = value`` based parsing.
+
+        Parameters
+        ----------
+        header_text : str
+            The full text of the file being parsed.
+        meta : dict
+            The metadata dictionary to update in place.
+
+        Returns
+        -------
+        dict
+            The updated metadata dictionary.
+        """
+        if "stype" not in metadata:
+            if re.search(r"(x-?ray|PDFgetX)", header_text, re.I):
+                metadata["stype"] = "X"
+            elif re.search(r"(neutron|PDFgetN)", header_text, re.I):
+                metadata["stype"] = "N"
+        regexes = {
+            "qmin": r"\bqmin *= *(%s)\b" % _FLOAT_RX,
+            "qmax": r"\bqmax *= *(%s)\b" % _FLOAT_RX,
+            "qdamp": r"\b(?:qdamp|qsig) *= *(%s)\b" % _FLOAT_RX,
+            "qbroad": r"\b(?:qbroad|qalp) *= *(%s)\b" % _FLOAT_RX,
+        }
+        for key, pattern in regexes.items():
+            if key in metadata:
+                continue
+            res = re.search(pattern, header_text, re.I)
+            if res:
+                metadata[key] = float(res.group(1))
+        return metadata
+
+
+# End of PDFParser

tests/conftest.py

@@ -72,3 +72,12 @@ def _datafile(filename):
         return importlib.resources.files("tests.testdata").joinpath(filename)
 
     return _datafile
+
+
+@pytest.fixture(scope="session")
+def as_list():
+    def _as_list(values):
+        """Unavailable uncertainties are None rather than an array."""
+        return None if values is None else values.tolist()
+
+    return _as_list